scholarly journals Background selection theory overestimates effective population size for high mutation rates

2022 ◽  
Author(s):  
Joseph D Matheson ◽  
Joanna Masel
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Deleterious Mutation ◽  
Neutral Theory ◽  
Mutation Rates ◽  
Background Selection ◽  
Effective Population ◽  
Selection Theory ◽  
Linkage Disequilibria ◽  
Genome Wide

Simple models from the neutral theory of molecular evolution are claimed to be flexible enough to incorporate the complex effects of background selection against linked deleterious mutations. Complexities are collapsed into an "effective" population size that specifies neutral genetic diversity. To achieve this, current background selection theory assumes linkage equilibrium among deleterious variants. Data do not support this assumption, nor do theoretical considerations when the genome-wide deleterious mutation is realistically high. We simulate genomes evolving under background selection, allowing the emergence of linkage disequilibria. With realistically high deleterious mutation rates, neutral diversity is much lower than predicted from previous analytical theory.

scholarly journals Does effective population size affect rates of molecular evolution: mitochondrial data for host/parasite species pairs in bees suggests not

2021 ◽  
Author(s):  
Nahid Shokri Bousjein ◽  
Simon Tierney ◽  
Michael Gardner ◽  
Michael Schwarz
Keyword(s):  
Molecular Evolution ◽  
Population Size ◽  
Effective Population Size ◽  
Parasite Species ◽  
Mitochondrial Protein ◽  
Neutral Theory ◽  
Mitochondrial Genes ◽  
Social Parasite ◽  
Effective Population ◽  
Rates Of Molecular Evolution

Adaptive evolutionary theory argues that organisms with larger effective population size (Ne) should have higher rates of adaptive evolution and therefore greater capacity to win evolutionary arm races. However, in some certain cases species with much smaller Ne may be able to survive beside their opponents for an extensive evolutionary time. Neutral theory predicts that accelerated rates of molecular evolution in organisms with exceedingly small Ne is due to the effects of genetic drift and fixation of slightly deleterious mutations. We test this prediction in two obligate social parasite species and their respective host species from the bee tribe Allodapini. The parasites (genus Inquilina) have been locked into a tight coevolutionary arm races with their exclusive hosts (genus Exoneura) for ~15 million years, even though Inquilina exhibit Ne that are an order of magnitude smaller than their host. In this study, we compared rates of molecular evolution between host and parasite using nonsynonymous to synonymous substitution rate ratios (dN/dS) of eleven mitochondrial protein coding genes sequenced from transcriptomes. Tests of selection on mitochondrial genes indicated no significant differences between host and parasite dN/dS, with evidence for purifying selection acting on all mitochondrial genes of host and parasite species. Several potential factors which could weaken the inverse relationship between Ne and rate of molecular evolution are discussed.

scholarly journals Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors

2020 ◽  
Vol 38 (1) ◽  
pp. 244-262
Author(s):  
Alexander T Ho ◽  
Laurence D Hurst
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Stop Codon ◽  
Neutral Theory ◽  
Error Rates ◽  
Species Variation ◽  
Effective Population ◽  
Weak Selection ◽  
Error Mitigation ◽  
Good Proxy

Abstract In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.

scholarly journals THE DYNAMICS OF FINITE HAPLOID POPULATIONS WITH OVERLAPPING GENERATIONS. II. THE DIFFUSION APPROXIMATION

Genetics ◽  
1979 ◽  
Vol 92 (1) ◽  
pp. 339-351
Author(s):  
Ted H Emigh
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Diffusion Approximation ◽  
Overlapping Generations ◽  
Mutation Rates ◽  
Reproductive Value ◽  
Selection Coefficient ◽  
Effective Population ◽  
Haploid Population

ABSTRACT The dynamics of a gene in a haploid population can be explained approximately by considering the average reproductive value of the gene. The dynamics of the average reproductive value are similar to those of a gene in a population with nonoverlapping generations with the following modifications: The effective population size, Ne, replaces N; the average mutation rates,μ* and v* replace μ and v; the average overall selection r*+(T-l)s** replaces s; and time is measured in terms of generations, T. The implications of the average selection coefficient to adaptive life histones are discussed.

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

scholarly journals Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0124157 ◽  
Author(s):  
Silvia Teresa Rodríguez-Ramilo ◽  
Jesús Fernández ◽  
Miguel Angel Toro ◽  
Delfino Hernández ◽  
Beatriz Villanueva
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Genome Wide ◽  
Holstein Population

scholarly journals Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens

2020 ◽  
Vol 37 (10) ◽  
pp. 2944-2954 ◽  
Author(s):  
Carina M Schlebusch ◽  
Per Sjödin ◽  
Gwenna Breton ◽  
Torsten Günther ◽  
Thijessen Naidoo ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Extreme Values ◽  
Homo Sapiens ◽  
Population Divergence ◽  
Effective Population ◽  
Genome Wide ◽  
Novel Variants ◽  
Paleoclimate Records ◽  
Unique Variation

Abstract The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

scholarly journals Evaluating the use of ABBA-BABA statistics to locate introgressed loci

2013 ◽  
Author(s):  
Simon H. Martin ◽  
John W. Davey ◽  
Chris D. Jiggins
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ancestral Population ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

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